#SpatialTranscriptomics

Loïc A. Royer 💻🔬🧪loicaroyer.bsky.social@bsky.brid.gy
2025-04-15

🧬🔬🧪 We are seeking a Scientist to push the limits of spatial transcriptomics in zebrafish! Come join us! #MolBio #SpatialTranscriptomics #DevelopmentalBiology #ScienceJobs 🧫🐟🔍 job-boards.greenhouse.io/chanzuckerbe...

Scientist, Spatial Molecular C...

Decoding cell–cell communication using spatial transcriptomics

#spatialtranscriptomics #omics #ccc
nature.com/articles/s41576-025

2025-02-28

📣 Listen up: you only have a few more days to apply for #EMBOSpatialOmics!

Would you like to get a comprehensive introduction to the various methods of spatial-omics and in particular those of multiplex immunofluorescence and spatial transcriptomics?

Then apply for this hands-on EMBO Practical Course by 10 March ✍️

🌍 EMBL Heidelberg
📅 15 – 20 June 2025
💻 s.embl.org/iso25-01-ma

#spatialtranscriptomics #microscopy #imageanalysis #spatialbiology #spatialomics

Benjamin S-B :verified:bensb@genomic.social
2024-09-17

#job alert: junior/mid-career PI opportunities in cancer research @ Oxford university: ludwig.ox.ac.uk/news/vacancies

Areas we're looking for:
#epigenetics #chromatin #epitranscriptomics #RNA #myeloidCells #spatialTranscriptomics

Please boost for visibility! @academicchatter #hiring

Thiago Carvalhocyrilpedia@qoto.org
2024-06-06

Tools (#preprint from 10x Genomics).
'Here, we introduce Visium HD Spatial Gene Expression (“Visium HD”) and demonstrate its use as a discovery platform for profiling CRC in multiple patients using FFPE tissue blocks. Visium HD slides provide a dramatically increased oligonucleotide barcode density over the Visium v2 slides (11,000,000 continuous features in a 6.5 mm Visium HD capture area, compared to 5,000 features with gaps between them in a 6.5 mm Visium v2 capture area). The single cell scale resolution of Visium HD allowed us to map distinct populations of immune cells, specifically macrophages and T cells, and evaluate differential gene expression at the tumor boundary to explore the potential contribution of these immune cell populations in the TME.'
#Immunology #Immunotherapy #SpatialTranscriptomics
biorxiv.org/content/10.1101/20

2023-09-28

Some really great talks and discussions today on advances in virus-livestock omics at the #Turing institute, who kindly supported the event. Talks include those by Ge Wu and Marie Di Placido (pictures) from the #Pirbright Institute.

Great to have input from the #BBSRC and #SFTC #Harttree Centre too.

Looking forward to new adventures in this area...

#livestock #virus #genomics #antibody #genome #mutation #pangenome #omics #transcriptomics #spatialtranscriptomics #fmdv

2023-09-20

Last chance to register for our meeting "Advancing virus-livestock omics" on Thurs 28th Sept at the Alan Turing Institute.

Registration closes end of Mon 25th.

See turing.ac.uk/events/advancing-

Register here: t.ly/wYA7d

Schedule below

Zoom stream possible for those from further afield

#livestock #virus #genomics #antibody #genome #mutation #pangenome #omics #transcriptomics #spatialtranscriptomics #fmdv

Pirbright-Turing meeting details
Marc Robinson-Rechavimarcrr@ecoevo.social
2023-09-12

Marius Lange #BC2basel: increasing complexity of #SingleCell data leads to problems of temporal, spatial and spatio-temporal mapping. The solution proposed is optimal transport applications, implemented in Moscot:
moscot.readthedocs.io/en/lates
biorxiv.org/content/10.1101/20 #SpatialTranscriptomics #scRNAseq

Marc Robinson-Rechavimarcrr@ecoevo.social
2023-09-12

Excellent conclusions of Jean Fan #BC2basel on #machinelearning applied to #scRNAseq #SpatialTranscriptomics

. Additional food for thought (for users)
Machine learning tools will always give you a solution  Whether the solution is reasonable must be evaluated with your expertise and human intelligence
Understanding where the data comes from, its LS and qualities, will allow you to evaluate whether a machine learning tool should be applied 
(automatically detected text)Additional food for thought (for developers) 
As machine learning is integrated into more sensitive domains like healthcare, we must emphasize: 
Transparent algorithms e open source: open code, open training data, reproducible 
Enables user judicial review 
Augmentation, not replacement 
(automatically detected text)
Marc Robinson-Rechavimarcrr@ecoevo.social
2023-09-12

Impressive work by Jean Fan's lab #BC2basel: aligning different spatial transcriptomics results, not only from different experiments but different protocols, e.g. MERFISH - Visium. Combining with #scRNAseq clustering and her lab's spot deconvolution allows to compare directly gene expression between these different experiments, biorxiv.org/content/10.1101/20 #SpatialTranscriptomics

Alessia Viscontialesssia@mas.to
2023-08-24

There is Minecraft. And then there is the #Visium manual fiducial alignment

#SpatialTranscriptomics #BioInformatics

C. Harris Floudaschfloudas@mstdn.social
2023-08-08

Excited for participating in this #spatialtranscriptomics #Visium platform study with an expert team from @NICHD_NIH, in the first step of studying the spatial biology of #pituitary corticotroph tumors, revealing their heterogeneity.

medrxiv.org/content/10.1101/20

2023-07-03

I might as well have make a pinned post.

We published Vesalius a tool that uses Image analysis methods to analyze spatial-omics data.

A new version will be coming soon that will include multimodal analysis and alignment!

GitHub: patrickcnmartin.github.io/Vesa

MSB: embopress.org/doi/full/10.1525

#SpatialTranscriptomics #ImageAnalysis

2023-06-04

O Psoriasis, a troubling foe,
We seek to know what causes your woes.
Your lesions so hard to manage
What makes them range?
Our search will make your secrets known.

#psoriasis #genetics #spatialtranscriptomics #research #ode #poetry

medicalnewstoday.com/articles/

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